siSPOTR specifications

Information


Unique identifier OMICS_04746
Name siSPOTR
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Publication for siSPOTR

siSPOTR in publications

 (8)
PMCID: 5754362
PMID: 29302059
DOI: 10.1038/s41467-017-02512-1

[…] sequences able to reduce mll1 mrna expression, sense and antisense 22-mer oligodeoxynucleotides (supplementary table ) encoding four different shrnas were designed using the online tool https://sispotr.icts.uiowa.edu/sispotr/index.html;jsessionid=245170f2742b69fb408f737cce6dac8f. the sense and antisense sequences were incorporated in silico (http://cancan.cshl.edu/cgi-bin/codex/tools.cgi) […]

PMCID: 5787672
PMID: 29387734
DOI: 10.1016/j.omtm.2017.12.005

[…] mechanism. nevertheless, we queried the sequences of each downregulated transcript identified by rna-seq against our mi405 and/or mi1155 guide and passenger strands using two different algorithms, sispotr and pita, to identify potential seed match binding sites., , , using this analysis, three transcripts had potential seed matches with mi1155, while two had predicted seeds for mi405 (). […]

PMCID: 5453866
PMID: 28603746
DOI: 10.1016/j.omtm.2017.05.001

[…] change > 1.5; p < 0.01; ). levels for none of the theoretical off-target transcripts mentioned above were significantly altered following pccl-h1-shhtt6 treatment. furthermore, we used the sispotr software to identify a list of potential targets of the seed sequence of shhtt6 in the 3′ utr of genes (“mir-like effect”) (). again, the top 100 genes obtained with sispotr were crossed […]

PMCID: 5402279
PMID: 28436437
DOI: 10.1038/srep46740

[…] anti-a: 5′-puuugauuuguagcagcagcuu-3′; rs362273 anti-g: 5′-puuugcucugcagcagcagcuu-3′; rs362307 anti-u: 5′-pcacacgggcacagacuuccaa-3′. the sirna sequence probability-of-off-targeting reduction (sispotr) algorithm (https://sispotr.icts.uiowa.edu/sispotr/index.html) was used to identify additional transcripts with the potential for off-target suppression. genes with an individual transcript […]

PMCID: 5281542
PMID: 28197125
DOI: 10.3389/fneur.2017.00013

[…] in mice., the goal of the present study was to test if virally mediated rnai decreased expression of human α-synuclein in mouse models. we used sirna sequence probability-of-off-targeting reduction (sispotr) tools to identify sirna sequences with minimal off-targeting potential and identified eight candidate sequences, labeled misyn1–8 (figure a; table ). we tested the efficacy of these eight […]


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siSPOTR institution(s)
Department of Internal Medicine, Program in Molecular and Cellular Biology, Institute for Clinical & Translational Science, University of Iowa, Iowa City, IA, USA

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